, 2021 at 11:32 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_convert problem
External Email - Use Caution
Dear List,
I have installed the ubuntu version of freesurfer (creating the VM as in the
tutorial)
I would like to run the following command:
mri_convert -c -oc 0 0 0
Thanks a lot!
Date: Fri, 15 Mar 2013 13:09:41 -0400
From: fis...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert problem
just:
mri_convert volume.mgz
cheers
Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote
: [Freesurfer] mri_convert problem
can you run ls -l and mri_info on it?
On Fri, 15 Mar 2013, Valtina Pouegue
wrote:
> I get this error-
> esther@m3012-04 ~]$ mri_info
> $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc
> mincRead(): can't find file/home/esther/Fre
convert direct from MNC to mgz^
Thanks
Date: Fri, 15 Mar 2013 10:00:04 -0400
From: fis...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert problem
can you run ls -l and mri_info on it?
On Fri, 15 Mar 2013, Valtina Pouegue
wrote
f20.m
nc
---I check in the directory enad the file is right there,
> Date: Fri, 15 Mar 2013 09:24:22 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: pval...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert problem
>
> Hi Valtina
&g
, 15 Mar 2013 09:24:22 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: pval...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert problem
>
> Hi Valtina
>
> you can convert directly without going through nii. What happens when you
>
Hi Valtina
you can convert directly without going through nii. What happens when you
run ls -l on that file? Or mri_info?
cheers
Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to mgz. But I
think I shoul first conver
Do you have read permission to the file? Also, you can convert straight
to mgz, not need to use nii as an intermediate.
doug
On 3/15/13 5:13 AM, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to
mgz. But I think I shoul first convert mnc to nii
Hi,
I have a problem of conversion. I would like to convert mnc file to mgz. But I
think I shoul first convert mnc to nii then nii to mgz. , so I try the command
mri_convert and I have this error; -[esther@m3012-04 ~]$
mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz
an I be sure that
> this will not change the handedness???'
>
> Bests,
> Gabriel
>
>
>
>
>
>
> > Date: Tue, 1 Feb 2011 10:59:56 -0500
> > From: gr...@nmr.mgh.harvard.edu
> > To: gabriel...@hotmail.com
> > CC: freesurfer@nmr.mgh.harvard.e
harvard.edu
> To: gabriel...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert problem
>
> There is a tag in this file that our DICOM reader does not recognize:
>
> 280092 DCM Unrecognized VR code (??) in readVRLength
>
> Unfortunately
There is a tag in this file that our DICOM reader does not recognize:
280092 DCM Unrecognized VR code (??) in readVRLength
Unfortunately, we're using a 3rd party dicom reader that is quite
brittle, and I don't know a way around it. Can you convert to nifti
using MRIcro and then use mri_convert
Rodrigo,
These appear to be from a NeuroLogica CereTom scanner, and while they
appear to be in dicom format, I cannot get mri_convert to recognize
them. However, mricro does read them, and can convert them to analyze
(which mri_convert can convert to .nii). Converting to analyze loses
orientatio
Hi,
I'm trying to run mri_convert to convert CT dicoms into nifti format but
I keep getting the following error:
[multnomah:CT] (nmr-std-env) mri_convert -i
1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii
mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii
file not found or
Problem:
mri_convert creates a NIFTI image that splits the dual echo, but pads
with empty slices to the full size, e.g. a dual echo of size 256 x
256 with 108 slices will become a 4D volume with 256 x 256 x 108 x 2
instead of 256 x 256 x 54 x 2. The -nth 0 or -nth 1 option will
return a
I can unpack these without a problem locally. Nick is preparing a new
minor stable release in which these fixes will be present.
doug
ps. If you just can't wait, you can get new versions of the following
(linux) binaries
mri_convert
mri_parse_sdcmdir
mri_probedicom
here:ftp://surfer.nmr.mg
Is this data on line here at the NMR center? Can you point me to it?
Dan Dillon wrote:
Dear FreeSurfers,
Our group has encountered an error while unpacking the first set of
data we acquired on Bay 2 since the upgrade. Here's our command line:
unpacksdcmdir -src 07120620/ -targ . -generic -
Dear FreeSurfers,
Our group has encountered an error while unpacking the first set of data we
acquired on Bay 2 since the upgrade. Here's our command line:
unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out
We then modify the .out file from
1localizer ok 512 51
Hi Jessica, it looks like you successfully ran this yesterday. Is this
still a problem?
doug
On Sat, 15 Sep 2007, Jessica Andrews-Hanna wrote:
Hi -
Does anyone know if there is a problem with mri_convert used within the
context of unpacksdcmdir? When I type the following at the command li
Hi -
Does anyone know if there is a problem with mri_convert used within
the context of unpacksdcmdir? When I type the following at the
command line (which we've used several times successfully in the past
in the Buckner lab):
ssh nexlin6
source /space/freesurfer/nmr-std-env
cd /space/ne
Dave,
It looks like a version of recon-all from 2004 is being used,
which predates the -i flag. Have you installed the newest
version of freesurfer (v3.0)? Or use mri_convert to create
the 001.mgz, 002.mgz input files in your /mri/orig
directory, and run recon-all from there.
Nick
> I am tryin
try running it with -debug and send along the output.
cheers,
Bruce
On Mon, 12 Jun 2006
[EMAIL PROTECTED] wrote:
I am trying to convert Dicom files to mgz format and I keep getting the
same error even when I try some variations on what I am typing in the
terminal. I have already set my subje
to convert Dicom files to mgz try to use following:
mri_convert -it dicom -i dicom_file -o your_file.mgz
to get more options type
mri_convert -- help
Silvester
[EMAIL PROTECTED] wrote:
I am trying to convert Dicom files to mgz format and I keep getting the
same error even when I try some v
I am trying to convert Dicom files to mgz format and I keep getting the
same error even when I try some variations on what I am typing in the
terminal. I have already set my subjects directory to
/home/amc/freesurferstable/subjects, which is where my first data set is
located, /1593-4. First I ch
does the output dir exists? Do you have write permission?
On Mon, 21 Nov
2005, Daniel Goldman wrote:
I've been getting this error message whenever I try to convert to .mgz
format:
mri_convert
/space/windu/4/users/recon/GORG25_recon/mri/32echo/magni
I've been getting this error message whenever I try to convert to .mgz
format:
mri_convert
/space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img
/space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/
Hi Scott,
this might be a work around, in case you need something quickly. I put some of
Soheil's matlab code into the mri_toolbox at http://eeg.sf.net/ and it should
read your GE data OK. See the ge_series_read, ge_series2avw and the avw2cor
functions, their documentation is available via the
have you tried specifying the input type? What error do you get?
Bruce
On 14 Jun
2004, Scott H. Johnson wrote:
> Hello,
>
> We are tryying to convert some raw images from our GE LX scanner into cor format
> using "mri_convert" with plans to do inflation etc.
>
>
> We have tried a number of w
Hello,
We are tryying to convert some raw images from our GE LX scanner into cor format using "mri_convert" with plans to do inflation etc.
We have tried a number of ways (see below) to no avail. The program tells us it is "reading images from 001/I.001," but never comes back. If anyone has
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